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Int. J. Mol. Sci. 2013, 14(1), 684-700; doi:10.3390/ijms14010684

A Molecular-Modeling Toolbox Aimed at Bridging the Gap between Medicinal Chemistry and Computational Sciences

Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
These authors contributed equally to this work.
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Author to whom correspondence should be addressed.
Received: 12 December 2012 / Revised: 21 December 2012 / Accepted: 26 December 2012 / Published: 4 January 2013
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

Abstract

In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand–protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.
Keywords: computer-aided drug discovery; structure-based design; multi-dimensional QSAR; molecular dynamics; single-click molecular modeling computer-aided drug discovery; structure-based design; multi-dimensional QSAR; molecular dynamics; single-click molecular modeling
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Eid, S.; Zalewski, A.; Smieško, M.; Ernst, B.; Vedani, A. A Molecular-Modeling Toolbox Aimed at Bridging the Gap between Medicinal Chemistry and Computational Sciences. Int. J. Mol. Sci. 2013, 14, 684-700.

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